NM_007051.3:c.114+5596C>T

Variant names:

• chr1-50852333-G-A
• rs1849553
• NM_007051.3:c.114+5596C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007051.3(FAF1):​c.114+5596C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,094 control chromosomes in the GnomAD database, including 4,444 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.23 (4444 hom., cov: 32)
• Consequence: FAF1 NM_007051.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231
• Publications: 9 publications found

Genes affected

FAF1 (HGNC:3578): (Fas associated factor 1) Interaction of Fas ligand (TNFSF6) with the FAS antigen (TNFRSF6) mediates programmed cell death, also called apoptosis, in a number of organ systems. The protein encoded by this gene binds to FAS antigen and can initiate apoptosis or enhance apoptosis initiated through FAS antigen. Initiation of apoptosis by the protein encoded by this gene requires a ubiquitin-like domain but not the FAS-binding domain. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAF1	NM_007051.3	c.114+5596C>T		intron_variant	Intron 2 of 18	ENST00000396153.7	NP_008982.1
FAF1	XM_024452734.2	c.90+5596C>T		intron_variant	Intron 2 of 18		XP_024308502.1
FAF1	XM_047442743.1	c.-148+5596C>T		intron_variant	Intron 3 of 19		XP_047298699.1
FAF1	XM_047442745.1	c.-148+5596C>T		intron_variant	Intron 3 of 19		XP_047298701.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAF1	ENST00000396153.7	c.114+5596C>T		intron_variant	Intron 2 of 18	1	NM_007051.3	ENSP00000379457.2
FAF1	ENST00000487898.1	n.136+5596C>T		intron_variant	Intron 2 of 6	3

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34864 AN: 151976 Hom.: 4442 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.292

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.229 AC: 34863 AN: 152094 Hom.: 4444 Cov.: 32 AF XY: 0.223 AC XY: 16615 AN XY: 74364

African (AFR) AF: 0.167 AC: 6915 AN: 41516

American (AMR) AF: 0.240 AC: 3657 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1226 AN: 3466

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5182

South Asian (SAS) AF: 0.244 AC: 1178 AN: 4820

European-Finnish (FIN) AF: 0.167 AC: 1766 AN: 10582

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19116 AN: 67946

Other (OTH) AF: 0.290 AC: 613 AN: 2112

Alfa AF: 0.271 Hom.: 2809

Bravo AF: 0.230

Asia WGS AF: 0.124 AC: 429 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.84
DANN	Benign	0.67
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1849553; hg19: chr1-51318005;